At this time Captain Barry was in command of the squadron in the lower Delaware River and in the Bay. By the destruction of the "Effingham" in the upper Delaware he was without a command other than the temporary one in which he was operating. Accordingly, on May 30, 1778, the Marine Committee appointed him to the command of the frigate "Raleigh," then in Boston Harbor. He was directed to "repair immediately to that place" to take command. He succeeded Captain Thomas Thompson, who was charged with having deserted the "Alfred" (Barry's old-time "Black Prince") in the battle with the British frigates "Ariadne" and "Ceres," by which the "Alfred" became captive. Captain Barry proceeded to Boston and, taking command of the "Raleigh," refitted her for service and went to sea, stopping at Rhode Island, where he received the orders of Marine Committee, on August 24, 1778, ordering him to cruise in company with the Continental brigantine "Resistance," Captain Burke, between Cape Henlopen and Occracok on the coast of North Carolina to intercept British armed vessels infesting that coast. On May 28th orders were sent to Hampton, Virginia, for delivery to Captain Barry, directing him to take under convoy six or more of the vessels loaded with commissary stores and protect them to the places of destination. Then he and Captain Burke were to proceed and protect the coast line of Virginia and North Carolina, reporting once a week at Hampton for orders, which he, as Senior Officer, should communicate to Captain Burke, and also there receive supplies furnished by the Governor of Virginia. Captain Barry in the "Raleigh" cruised along the coast from North Carolina to Massachusetts Bay. On September 8, 1778, off Boston Bay he reported to the Marine Committee that many of the guns of the "Raleigh" had burst in proving and the ship was "exceedingly foul" and unfit to further cruise. He was, on September 28, 1778, directed to proceed to Portsmouth, Virginia, where there was a Continental shipyard, and have the "Raleigh's" bottom cleaned. That done he was to continue "to cruise upon the coast," the "Deane" or any other vessel with him, Barry was to order to cruise while the "Raleigh" was being cleaned. The Committee had information that the British frigate "Persius," of 32 guns was cruising singly on the coast of South Carolina. Barry was then ordered as soon as his ship was cleaned to extend his cruising ground so as to cover the coast of that State, taking the "Deane" or other vessel with him in search of the "Persius" and endeavor to "take, burn, sink or destroy" the said frigate or any other of the enemy's vessels "that he might fall in with." If he made a capture he was to take it to Charleston and there fit, man her and take her on the cruise with him.